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作物学报

作物学报 ›› 2022, Vol. 48 ›› Issue (12): 3045-3056.doi: 10.3724/SP.J.1006.2022.12080

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

水稻氮高效基因分子标记开发与基因型筛选

陶亚军1,3(), 朱静妍2, 王军1,3, 范方军1,3, 许扬1,3, 李文奇1,3, 王芳权1,3, 陈智慧1,3, 蒋彦婕1,3, 朱建平1,3, 李霞1,3, 杨杰1,3()   

  1. 1江苏省农业科学院粮食作物研究所 / 国家水稻改良中心南京分中心 / 江苏省优质水稻工程技术研究中心, 江苏南京 210014
    2扬州大学生物科学与技术学院, 江苏扬州 225009
    3扬州大学 / 江苏省粮食作物现代产业技术协同创新中心, 江苏扬州 225009
  • 收稿日期:2021-11-29 接受日期:2022-03-25 出版日期:2022-12-12 网络出版日期:2022-04-20
  • 通讯作者: 杨杰
  • 作者简介:E-mail: ricetao@163.com
  • 基金资助:
    江苏省重点研发计划项目(BE2020339);江苏省青年基金项目(BK20190255);国家青年科学基金项目(31901525);江苏省重点研发计划项目(BE2021374);国家自然科学基金国际(地区)合作与交流项目(31861143011);江苏省农业科技资助创新资金项目(CX(19)1002)

Development of functional markers and genotype screening for nitrogen use efficiency genes in rice

TAO Ya-Jun1,3(), ZHU Jing-Yan2, WANG Jun1,3, FAN Fang-Jun1,3, XU Yang1,3, LI Wen-Qi1,3, WANG Fang-Quan1,3, CHEN Zhi-Hui1,3, JIANG Yan-Jie1,3, ZHU Jian-Ping1,3, LI Xia1,3, YANG Jie1,3()   

  1. 1Jiangsu High Quality Rice Center / Nanjing Branch of Chinese National Center for Rice Improvement / Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
    2College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, Jiangsu, China
    3Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Yangzhou University, Yangzhou 225009, Jiangsu, China
  • Received:2021-11-29 Accepted:2022-03-25 Published:2022-12-12 Published online:2022-04-20
  • Contact: YANG Jie
  • Supported by:
    Jiangsu Province Key Research and Development Program Modern Agriculture(BE2020339);Natural Science Foundation of Jiangsu Province(BK20190255);National Natural Science Foundation of China(31901525);Jiangsu Province Key Research and Development Program Modern Agriculture(BE2021374);International Cooperation and Exchange of the National Natural Science Foundation of China(31861143011);Jiangsu Agricultural Science and Technology Innovation Fund(CX(19)1002)

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摘要：

氮素是促进水稻物质生产和产量形成的首要因素, 其高效与合理的利用是农业可持续发展的重要保障。培育含有氮高效基因的水稻品种, 充分发挥氮素高效吸收和利用遗传潜力是提高氮肥利用率、减少氮肥施用量的有效途径。本研究从氮素的吸收、转运、再分配和再利用等环节, 选择了OsNR2、OsNPF6.1、OsTCP19、OsLHT1和OsGRF4共5个基因作为水稻氮高效遗传改良的基因组合, 根据已报道的功能位点设计得到与目标基因共分离的基因功能标记, 包括6对等位特异PCR标记和1对InDel标记, 并对70份常规籼稻, 34份常规粳稻和84份太湖资源水稻材料进行了鉴定。结果表明, OsNR2在籼稻中分布较广, OsNPF6.1、OsTCP19、OsGRF4在籼稻中分布较少, 但是均未在常规粳稻中检出; 常规粳稻中仅含有OsLHT1; 同时我们还筛选出2份材料同时含有OsNR2、OsNPF6.1和OsGRF4高效单倍型。本研究开发的功能标记和筛选出的材料为通过分子标记辅助选择方法培育氮高效水稻新品种提供了技术支撑。

关键词: 水稻, 氮高效利用, 等位特异PCR标记, InDel标记

Abstract:

Nitrogen is an essential mineral element that affects plants biomass and yield formation, and its efficient and reasonable utilization is an important guarantee for sustainable agricultural. Breeding rice varieties containing high nitrogen use efficiency (NUE) genes is an effective way to increase NUE and reduce the amount of nitrogen fertilizer. In this study, five genes, OsNR2, OsNPF6.1, OsTCP19, OsLHT1, and OsGRF4, were selected from the aspects of nitrogen absorption, transportation, and assimilation. Based on the reported functional haplotype, co-segregated markers were designed. Using six pairs of allele-specific PCR (AS-PCR) markers and one pair of InDel marker, 70 indica rice, 34 japonica rice, and 84 Taihu rice resources were identified. The results showed that OsNR2 was widely distributed in indica rice, while OsNPF6.1, OsTCP19, and OsGRF4 were less distributed. All 34 japonica rice and 84 Taihu rice resources only contained OsLHT1. We also successfully obtained two indica germplasms, which contained OsNR2, OsNPF6.1, and OsGRF4. The functional markers developed in this research and two materials provide technical support for breeding new rice varieties with high NUE through molecular marker-assisted selection (MAS) methods.

Key words: rice, high nitrogen-use efficiency, AS-PCR, InDel markers

表1

水稻氮高效基因功能标记引物"

引物名称
Primer name		 引物序列
Primer sequence (5'-3')		 PCR片段大小
PCR fragment (bp)
NR2-F AGGGCGAGGACCCCAAGT
NR2-R GTCGTCGGGCTGGTCCCA 242
nr2-R GTCGTCGGGCTGGTCCCT 242
NPF6.1-F ATTATGGAACGGAGGGAG
NPF6.1-R CCCGGATGTCCACAACAC 246
npf6.1-R CCCGGATGTCCACAACAT 246
TCP19-INDEL-F TAACTCTTCAGGGTTCTTGC
TCP19-INDEL-R TGTGCCGTGTCACATAGA 253
LHT1-1-F GTTGCGGCTGACAATAAA
LHT1-1-R AGCATGGGGTCAAAGCAA 317
lht1-1-R AGCATGGGGTCAAAGCAG 317
LHT1-2-F TCATAATGCTTACCCTCT
LHT1-2-R TGGAGGGTTGACTCGTAA 166
lht1-2-R TGGAGGGTTGACTCGTAT 166
GRF4-1-F AACCAAATAAGCCCTTCA
GRF4-1-R ATGTGATAAAAAAGCTGTAA 329
grf4-1-R ATGTGATAAAAAAGCTGTAT 329
GRF4-2-F AACCAAATAAGCCCTTCA
GRF4-2-R TAGTTCACGCTAAAATTAG 410
grf4-2-R TAGTTCACGCTAAAATTAA 410

图1

水稻氮高效基因功能分类和变异位点 A: 氮高效基因的功能分类; B: 氮高效基因功能变异位点。"

图2

不同功能标记的扩增效果 泳道1, 3: NR2标记; 2, 4: nr2标记; 5, 7: NPF6.1标记; 6, 8: npf6.1标记; 9, 11: LHT1-1标记; 10, 12: lht1-1标记; 13, 15: LHT1-2标记; 14, 16: lht1-2标记; 17, 19: GRF4-1标记; 18, 20: grf4-1标记; 21, 23: GRF4-2标记; 22, 24: grf4-2标记; 25: TCP19-INDEL在‘日本晴’中扩增条带; 26: TCP19-INDEL在‘Ksalath’中扩增条带。M: DL2000 marker。"

表2

水稻氮高效基因功能标记扩增亲本及位点"

标记名称
Marker name		 扩增亲本
Amplification parent		 扩增位点
Amplification site
NR2 NIP OsNR2779T
nr2 9311 OsNR2779A
NPF6.1 NIP OsNPF6.1160G
npf6.1 NJ11 OsNPF6.1160A
TCP19 NIP, Kasalath OsTCP启动子区29 bp的InDel A 29 bp InDel in the OsTCP19 promoter
LHT1-1 NIP OsLHT1-2140T
lht1-1 9311 OsLHT1-2140C
LHT1-2 NIP OsLHT1-595T
lht1-2 9311 OsLHT1-595A
GRF4-1 NIP OsGRF4-884T
grf4-1 RD23 OsGRF4-884A
GRF4-2 NIP OsGRF4-801C
grf4-2 RD23 OsGRF4-801T

表3

氮高效基因在常规籼稻中分布"

材料Material OsNR2 OsNPF6.1 OsTCP19 OsLHT1-1 OsLHT1-2 OsGRF4-1 OsGRF4-2
951227 1 1 0 0 0 1 1
南京16 Nanjing 16 1 1 0 0 0 1 1
Z03108 1 1 0 0 0 0 0
04-286 1 1 0 0 0 0 0
扬稻8号 Yangdao 8 1 1 0 0 0 0 0
扬州98127 Yangzhou 98127 1 1 0 0 0 0 0
9311 1 1 0 0 0 0 0
中佳2号 Zhongjia 2 1 1 0 0 0 0 0
苏农3004 Sunong 3004 1 1 0 0 0 0 0
扬籼9850 Yangxian 9850 1 1 0 0 0 0 0
R6547 1 1 0 0 0 0 0
R6548 1 1 0 0 0 0 0
镇籼886 Zhenxian 886 1 0 0 0 0 0 0
IRRI超高产系 IRRI super high-yield line 1 0 0 0 0 0 0
金桂占选 Jinguizhanxuan 1 0 0 0 0 1 1
广超丝苗 Guangchaosimiao 1 0 0 0 0 0 0
玉香油占 Yuxiangyouzhan 1 0 0 0 0 0 0
银花占2号 Yinhuazhan 2 1 0 0 0 0 0 0
丰华占 Fenghuazhan 1 0 0 0 0 0 0
茉莉软占 Moliruanzhan 1 0 0 0 0 0 0
黄华占 Huanghuazhan 1 0 0 0 0 0 0
五山油占 Wushanyouzhan 1 0 1 0 0 0 0
茉莉丝占 Molisizhan 1 0 0 0 0 0 0
矮秀占 Aixiuzhan 1 0 0 0 0 0 0
茉莉油占 Moliyouzhan 1 0 0 0 0 0 0
丰新占 Fengxinzhan 1 0 1 0 0 0 0
黄美占 Huangmeizhan 1 0 0 0 0 0 0
黄莉占 Huanglizhan 1 0 0 0 0 0 0
黄丝占 Huangsizhan 1 0 0 0 0 0 0
丰二占 Feng’erzhan 1 0 0 0 0 0 0
华新占 Huaxinzhan 1 0 0 0 0 0 0
新514 Xin 514 1 1 0 0 0 0 0
R9912 1 0 0 0 0 1 1
浙恢7954 Zhehui 7954 1 0 0 0 0 0 0
泸恢17 Luhui 17 1 1 0 0 0 0 0
蜀恢881 Shuhui 881 1 0 0 0 0 0 0
恢76 Hui76 1 0 0 0 0 0 0
辐恢718 Fuhui 718 1 0 0 0 0 0 0
内香恢1号 Neixianghui 1 1 1 0 0 0 0 0
内多恢1号 Neiduohui 1 1 1 0 0 0 0 0
盐恢559 Yanhui 559 1 0 0 0 0 0 0
川恢725 Chuanhui 725 1 0 0 0 0 0 0
广恢128 Guanghui 128 1 0 0 0 0 0 0
湘747 Xiang 747 1 0 0 0 0 0 0
丰籼1号 Fengxian 1 1 0 0 0 0 0 0
小农占 Xiaonongzhan 1 0 0 0 0 0 0
五山丝苗 Wushansimiao 1 0 0 0 0 0 0
黄花占 Huanghuazhan 1 0 0 0 0 0 0
粤香占 Yuexiangzhan 1 0 0 0 0 0 0
粤禾丝苗 Yuehesimiao 1 1 0 0 0 0 0
粤综占 Yuezongzhan 1 1 0 0 0 0 0
粤农丝苗 Yuenongsimiao 1 1 0 0 0 0 0
金农丝苗 Jinnongsimiao 1 0 0 0 0 0 0
宁317 Ning 317 1 0 0 0 0 0 0
南农3017 Nannong 3017 1 1 0 0 0 0 0
泸恢195 Luhui 195 1 0 0 0 0 0 0
泸恢17 Luhui 17 1 0 0 0 0 0 0
桂99 Gui 99 1 0 0 0 0 0 0
辐恢838 Fuhui 838 1 0 0 0 0 0 0
Basmati-1 1 0 0 0 0 0 0
成恢149 Chenghui 149 1 0 0 0 0 0 0
绵恢725 Mianhui 725 1 1 0 0 0 0 0
E32辐照选-15 E32 radiation-15 1 1 0 0 0 0 0
成恢22 Chenghui 22 1 1 0 0 0 0 0
中香11 Zhongxiang 11 1 0 0 0 0 1 1
L30012 1 1 0 0 0 0 0
新513 Xin 513 1 0 0 0 0 0 0
胜泰1号 Shengtai 1 1 0 0 0 0 0 0
L30015 1 0 0 0 0 0 0
Kasalath 1 1 0 0 0 0 0

表4

氮高效基因在常规粳稻中分布"

材料Material OsNR2 OsNPF6.1 OsTCP19 OsLHT1-1 OsLHT1-2 OsGRF4-1 OsGRF4-2
连粳7号 Lianjing 7 0 0 0 1 1 0 0
连粳10号 Lianjing 10 0 0 0 1 1 0 0
徐稻3号 Xudao 3 0 0 0 1 1 0 0
淮稻5号 Huaidao 5 0 0 0 0 0 0 0
盐稻8号 Yandao 8 0 0 0 0 0 0 0
扬育粳2号 Yangyujing 2 0 0 0 1 1 0 0
扬9709 Yang 9709 0 0 0 1 1 0 0
扬中稻1号 Yangzhongdao 1 0 0 0 1 1 0 0
武陵粳1号 Wulingjing 1 0 0 0 1 1 0 0
扬辐粳1号 Yangfujing 1 0 0 0 1 1 0 0
宁粳1号 Ningjing 1 0 0 0 1 1 0 0
南粳49 Nanjing 49 0 0 0 1 1 0 0
南粳46 Nanjing 46 0 0 0 1 1 0 0
南粳5055 Nanjing 5055 0 0 0 1 1 0 0
苏沪香粳 Suhuxiangjing 0 0 0 1 1 0 0
武香粳14号 Wuxiangjing 14 0 0 0 1 1 0 0
武运粳7号 Wuyunjing 7 0 0 0 1 1 0 0
武运粳23号 Wuyunjing 23 0 0 0 1 1 0 0
苏香粳2号 Suxiangjing 2 0 0 0 1 1 0 0
嘉33 Jia 33 0 0 0 1 1 0 0
嘉991 Jia 991 0 0 0 1 1 0 0
镇稻1号 Zhendao 1 0 0 0 1 1 0 0
日辉粳6号 Rihuijing 6 0 0 0 0 0 0 0
泗阳紫稻 Siyangzidao 0 0 0 1 1 0 0
楚粳39 Chujing 39 0 0 0 0 0 0 0
云光104 Yunguang 104 0 0 0 1 1 0 0
粳优165 Jingyou 165 0 0 0 1 1 0 0
小粒香 Xiaolixiang 0 0 0 1 1 0 0
越光BL Yueguang BL 0 0 0 1 1 0 0
苏秀867 Suxiu 867 0 0 0 1 1 0 0
苏垦118 Suken 118 0 0 0 0 0 0 0
东北194 Dongbei 194 0 0 0 1 1 0 0
临稻16 Lindao 16 0 0 0 1 1 0 0
降糖稻 Jiangtangdao 0 0 0 0 0 0 0

表5

氮高效基因在太湖资源中分布"

材料Material NR2 NPF6.1 TCP19 LHT1-1 LHT1-2 GRF4-1 GRF4-2
抱芯太湖青 Baoxintaihuqing 0 0 0 1 1 0 0
矮脚太湖青 Aijiaotaihuqing 0 0 0 1 1 0 0
上海青 Shanghaiqing 0 0 0 1 1 0 0
海冬青 Haidongqing 0 0 0 1 1 0 0
常梗青 Changenqing 0 0 0 1 1 0 0
立更青 Ligengqing 0 0 0 1 1 0 0
齐江青 Qijiangqing 0 0 0 1 1 0 0
矮种罗汉黄 Aizhongluohanhuang 0 0 0 1 1 0 0
呆长青 Daichangqing 0 0 0 1 1 0 0
万年青 Wannianqing 0 0 0 1 1 0 0
韭菜青 Jiucaiqing 0 0 0 1 1 0 0
茭白叶青 Jiaobaiyeqing 0 0 0 1 1 0 0
大红稻(老来红) Dahongdao 0 0 0 1 1 0 0
老头老来红 Laotoulaolaihong 0 0 0 1 1 0 0
早黑头红 Zaoheitouhong 0 0 0 1 1 0 0
晚罗汉稻 Wanluohandao 0 0 0 1 1 0 0
晚牛毛黄 Wanniumaohuang 0 0 0 1 1 0 0
TH93 0 0 0 1 1 0 0
白石稻 Baishidao 0 0 0 1 1 0 0
大量稻 Daliangdao 0 0 0 1 1 0 0
白薄稻 Baibodao 0 0 0 1 1 0 0
二黑稻 Eeheidao 0 0 0 1 1 0 0
摧稻 Cuidao 0 0 0 1 1 0 0
红虹稻 Hongxiadao 0 0 0 1 1 0 0
鹅营白粳稻 Eyingbaijingdao 0 0 0 1 1 0 0
大穗头粳稻 Dasuitoujingdao 0 0 0 1 1 0 0
矮子粳稻 Aizijingdao 0 0 0 1 1 0 0
长黄稻 Changhuangdao 0 0 0 1 1 0 0
矮黄稻 Aihuangdao 0 0 0 1 1 0 0
减晚慢种 Jianwanmanzhong 0 0 0 1 1 0 0
天下第一种 Tianxiadiyizhong 0 0 0 1 1 0 0
红芒种 Hongmangzhong 0 0 0 1 1 0 0
矮洁种 Aijiezhong 0 0 0 1 1 0 0
瓜田种 Guatianzhong 0 0 0 1 1 0 0
龙沟种 Longgouzhong 0 0 0 1 1 0 0
老大种 Laodazhong 0 0 0 1 1 0 0
老虎种 Laohuzhong 0 0 0 1 1 0 0
余山种 Yushanzhong 0 0 0 1 1 0 0
TH262 0 0 0 1 1 0 0
江北种 Jiangbeizhong 0 0 0 1 1 0 0
TH274 0 0 0 1 1 0 0
TH275 0 0 0 1 1 0 0
白稻头 Baidaotou 0 0 0 1 1 0 0
TH284 0 0 0 1 1 0 0
TH301 0 0 0 1 1 0 0
TH303 0 0 0 1 1 0 0
TH324 0 0 0 1 1 0 0
TH345 0 0 0 1 1 0 0
TH346 0 0 0 1 1 0 0
TH359 0 0 0 1 1 0 0
不留名 Buliuming 0 0 0 1 1 0 0
TH369 0 0 0 1 1 0 0
甩杀极 Shuaishaji 0 0 0 1 1 0 0
TH373 0 0 0 1 1 0 0
TH374 0 0 0 1 1 0 0
TH376 0 0 0 1 1 0 0
TH380 0 0 0 1 1 0 0
TH382 0 0 0 1 1 0 0
TH384 0 0 0 1 1 0 0
TH385 0 0 0 1 1 0 0
南束罗汉黄 Nanshuluohanhuang 0 0 0 1 1 0 0
润叶黄 Runyehuang 0 0 0 1 1 0 0
TH390 0 0 0 1 1 0 0
有芒旱稻 Youmanghandao 0 0 0 1 1 0 0
TH394 0 0 0 1 1 0 0
TH403 0 0 0 1 1 0 0
TH407 0 0 0 1 1 0 0
TH413 0 0 0 1 1 0 0
六十子粳 Liushizijing 0 0 0 1 1 0 0
东方红1号(穗1) Dongfanghong 1 0 0 0 1 1 0 0
小红早 Xiaohongzao 0 0 0 1 1 0 0
润叶黄 Runyehuang 0 0 0 1 1 0 0
早小白稻 Zaoxiaobaidao 0 0 0 1 1 0 0
抖山旱稻(陆稻) Doushanhandao 0 0 0 1 1 0 0
早飞来风 Zaofeilaifeng 0 0 0 1 1 0 0
一时兴 Yishixing 0 0 0 1 1 0 0
头等一时兴 Toudengyishixing 0 0 0 1 1 0 0
香粳糯稻 Xiangjingnuodao 0 0 0 1 1 0 0
TH433 0 0 0 1 1 0 0
TH434 0 0 0 1 1 0 0
TH436 0 0 0 1 1 0 0
红芒糯 Hongmangnuo 0 0 0 1 1 0 0
TH438 0 0 0 1 1 0 0
TH444 0 0 0 1 1 0 0

表6

水稻氮高效基因测序引物及变异位点分析"

引物名称 Primer name 引物序列 Primer sequence (5'-3')
NR2-CX F: AGGGCGAGGACCCCAAGT; R: TGTCGAGGTCATAGCCCATCTT
NPF6.1-CX F: ATTATGGAACGGAGGGAG; R: GGAGATAGAGGGTGGTGAA
TCP19-CX F: TAACTCTTCAGGGTTCTTGC; R: TGTGCCGTGTCACATAGA
LHT1-1-CX F: GTTGCGGCTGACAATAAA; R: AATCTCGTGGGAAATCTG
LHT1-2-CX F: TCATAATGCTTACCCTCT; R: TTGTTTTGCTAACTCACA
GRF4-CX F: AACCAAATAAGCCCTTCA; R: TTAGTCTGCTGCTCCAAC

图3

部分水稻品种氮高效基因功能位点序列比对. A: 9311中OsNR2功能序列; B: R6547中OsNPF6.1功能序列; C: 苏垦118中OsLHT1-1功能序列; D: 淮稻5号中OsLHT1-2功能序列; E: 金桂占选中OsGRF4-1功能序列; F: 南京16中OsGRF4-2功能序列; G: 五山油占中OsTCP19功能序列。红色框表示差异碱基或序列。"

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